XTEND: Extending the depth of field in cryo soft X-ray tomography

We have developed a new data collection method and processing framework in full field cryo soft X-ray tomography to computationally extend the depth of field (DOF) of a Fresnel zone plate lens. Structural features of 3D-reconstructed eukaryotic cells that are affected by DOF artifacts in standard reconstruction are now recovered. This approach, based on focal series projections, is easily applicable with closed expressions to select specific data acquisition parameters.

[1]  一岡 芳樹,et al.  J. D. Gaskill: Linear Systems, Fourier Transforms, and Optics, John Wiley & Sons, New York, 1978, xiv+554ページ, 23.5×15.5cm, $24.96 (Wiley Sons in Pure and Applied Optics). , 1979 .

[2]  Max Born,et al.  Principles of optics - electromagnetic theory of propagation, interference and diffraction of light (7. ed.) , 1999 .

[3]  A. Papoulis.  Linear systems, Fourier transforms, and optics , 1981, Proceedings of the IEEE.

[4]  N. Streibl.  Depth Transfer by an Imaging System , 1984 .

[5]  J Bille,et al.  Reconstructing 3-D light-microscopic images by digital image processing. , 1985, Applied optics.

[6]  J. Kirz,et al.  Soft X-ray microscopes and their biological applications , 1995, Quarterly Reviews of Biophysics.

[7]  J R Kremer,et al.  Computer visualization of three-dimensional image data using IMOD. , 1996, Journal of structural biology.

[8]  A G Valdecasas,et al.  On the extended depth of focus algorithms for bright field microscopy. , 2001, Micron.

[9]  S. Gabarda,et al.  Blind image quality assessment through anisotropy. , 2007, Journal of the Optical Society of America. A, Optics, image science, and vision.

[10]  M. Howells,et al.  A soft X-ray beamline for transmission X-ray microscopy at ALBA. , 2009, Journal of synchrotron radiation.

[11]  Gerry McDermott,et al.  Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans , 2009, Proceedings of the National Academy of Sciences.

[12]  José-Jesús Fernández,et al.  Fast tomographic reconstruction on multicore computers , 2011, Bioinform..

[13]  W. Chao,et al.  Real space soft x-ray imaging at 10 nm spatial resolution. , 2012, Optics express.

[14]  Kai Zhang,et al.  Extended depth of focus for transmission x-ray microscope. , 2012, Optics letters.

[15]  R. Glaeser,et al.  Focused issue on X-ray microscopy of biological materials. , 2012, Journal of structural biology.

[16]  Roberto Marabini,et al.  Image formation in cellular X-ray microscopy. , 2012, Journal of structural biology.

[17]  Sergio Marco,et al.  Three-Dimensional Chemical Mapping by EFTEM-TomoJ Including Improvement of SNR by PCA and ART Reconstruction of Volume by Noise Suppression , 2013, Microscopy and Microanalysis.

[18]  J M Carazo,et al.  Xmipp 3.0: an improved software suite for image processing in electron microscopy. , 2013, Journal of structural biology.

[19]  G. Herman,et al.  The soft x-ray transform , 2014 .

[20]  Elizabeth A. Smith,et al.  Correlative cryogenic tomography of cells using light and soft x-rays. , 2014, Ultramicroscopy.

[21]  T. Zeev-Ben-Mordehai,et al.  A cool hybrid approach to the herpesvirus ‘life’ cycle☆ , 2014, Current opinion in virology.

[22]  S. Rehbein,et al.  Multimodal nanoparticles as alignment and correlation markers in fluorescence/soft X-ray cryo-microscopy/tomography of nucleoplasmic reticulum and apoptosis in mammalian cells , 2014, Ultramicroscopy.

[23]  N. Sochen,et al.  3d Simulation of the Image Formation in Soft X- Ray Microscopes References and Links , 2022 .

[24]  L. Collinson,et al.  Imaging endosomes and autophagosomes in whole mammalian cells using correlative cryo-fluorescence and cryo-soft X-ray microscopy (cryo-CLXM)☆ , 2014, Ultramicroscopy.

[25]  L. Collinson,et al.  Correlative cryo-fluorescence and cryo-soft X-ray tomography of adherent cells at European synchrotrons. , 2014, Methods in cell biology.

[26]  G. Herman,et al.  Reconstruction from Microscopic Projections with Defocus-Gradient and Attenuation Effects , 2014 .

[27]  K. Grünewald,et al.  Critical step-by-step approaches toward correlative fluorescence/soft X-ray cryo-microscopy of adherent mammalian cells. , 2014, Methods in cell biology.

[28]  H. Hertz,et al.  Tomographic reconstruction in soft x-ray microscopy using focus-stack back-projection. , 2015, Optics letters.

[29]  J. Carazo,et al.  Measurement of the modulation transfer function of an X-ray microscope based on multiple Fourier orders analysis of a Siemens star. , 2015, Optics express.

[30]  J. Nicolas,et al.  MISTRAL: a transmission soft X-ray microscopy beamline for cryo nano-tomography of biological samples and magnetic domains imaging. , 2015, Journal of synchrotron radiation.

[31]  J. Carrascosa,et al.  Structural Changes In Cells Imaged by Soft X-ray Cryo-Tomography During Hepatitis C Virus Infection. , 2016, ACS nano.

[32]  J. Carazo,et al.  Characterization of transfer function, resolution and depth of field of a soft X-ray microscope applied to tomography enhancement by Wiener deconvolution. , 2016, Biomedical optics express.

[33]  L. Addadi,et al.  Development of Correlative Cryo-soft X-ray Tomography and Stochastic Reconstruction Microscopy. A Study of Cholesterol Crystal Early Formation in Cells. , 2016, Journal of the American Chemical Society.

[34]  José L Carrascosa,et al.  Intracellular nanoparticles mass quantification by near-edge absorption soft X-ray nanotomography , 2016, Scientific Reports.